Background: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription.However, the method cannot accurately estimate duplicated genes expression. Several strategies have beenpreviously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of themprovide biased results.Results: We provide here a tool, called mmquant, for computing gene expression, included duplicated genes. If aread maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes.Conclusion: mmquant is a drop-in replacement of the widely used tools htseq-count and featureCounts thathandles multi-mapping reads in an unabiased way.
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